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  • Ericsson, Olle, et al. (författare)
  • Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.
  • 2019
  • Ingår i: Prenatal diagnosis. - 1097-0223. ; 39:11, s. 1011-1015
  • Tidskriftsartikel (refereegranskat)abstract
    • To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening.
  • Persson, Fredrik, et al. (författare)
  • 2017
  • Ingår i: 2017 WINTER SIMULATION CONFERENCE (WSC). - IEEE. - 978-1-5386-3428-8 ; s. 3768-3779
  • Konferensbidrag (refereegranskat)abstract
    • Safety stock calculations are difficult for products with intermittent demand, long production lead times, and high monetary values. Theoretically, forecasts can be used to reduce the need for safety stocks. A high precision forecast minimizes the need for safety stock and forecast evaluation measurements can be used to calculate the safety stock level. However, a more realistic determination of safety stock levels can he obtained by simulation. In this paper, simulation is used to model and experiment on a case with three end products in order to determine the relationship between safety stock levels and service levels. Also, a comparison is made with theoretically calculated safety stocks to see how well basic theoretical models for safety stock calculations fulfill the requirements of service level. The result is that simulation can provide a much more accurate determination of safety stock levels for intermittent demands than theoretical calculations.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
  • 2015
  • Ingår i: Macromolecules. - The American Chemical Society (ACS). - 0024-9297. ; 48:3, s. 871-878
  • Tidskriftsartikel (refereegranskat)abstract
    • Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Unfolding of nanoconfined circular DNA
  • 2015
  • Ingår i: BIOPHYSICAL JOURNAL. - 0006-3495. ; 108:2 Supplement 1, s. 231A-231A
  • Tidskriftsartikel (övrigt vetenskapligt)
  • Asp, Michaela, et al. (författare)
  • Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
  • 2017
  • Ingår i: Scientific Reports. - NATURE PUBLISHING GROUP. - 2045-2322 .- 2045-2322. ; 7
  • Tidskriftsartikel (refereegranskat)abstract
    • Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.
  • Espinoza, Fredrik, et al. (författare)
  • Analysis of Open Answers to Survey Questions throughInteractive Clustering and Theme Extraction
  • 2018
  • Ingår i: Proceedings of Conference on Human Information Interaction & Retrieval. - ACM Digital Library. ; s. 317-320
  • Konferensbidrag (refereegranskat)abstract
    • This paper describes design principles for and the implementation of Gavagai Explorer—a new application which builds on interactive text clustering to extract themes from topically coherent text sets such as open text answers to surveys or questionnaires.An automated system is quick, consistent, and has full coverage over the study material. A system allows an analyst to analyze more answers in a given time period; provides the same initial results regardless of who does the analysis, reducing the risks of inter-rater discrepancy; and does not risk miss responses due to fatigue or boredom. These factors reduce the cost and increase the reliability of the service. The most important feature, however, is relieving the human analyst from the frustrating aspects of the coding task, freeing the effort to the central challenge of understanding themes. Gavagai Explorer is available on-line at http://explorer.gavagai.se
  • Fornander, Louise H., et al. (författare)
  • Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels
  • 2016
  • Ingår i: Langmuir. - 07437463. ; 32:33, s. 8403-8412
  • Tidskriftsartikel (refereegranskat)abstract
    • RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg2+ or Ca2+), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
  • Heyman, Fredrik, et al. (författare)
  • Has the Swedish business sector become more entrepreneurial than the US business sector?
  • 2019
  • Ingår i: Research Policy. - Elsevier. - 0048-7333. ; 48:7, s. 1809-1822
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent studies document a 30-year decline in various measures of entrepreneurship in the U.S. Using detailed Swedish employer-employee data over the period from 1990 to 2013, we find young firms to be more prominent in the Swedish business sector than in the U.S. business sector. Young Swedish firms, aged five years or less, account for more than half of all firms during this period. We also observe an increase in Swedish entrepreneurial activity for start-ups. However, since the mid-2000s, job destruction rates for young firms have been increasing, which implies a declining employment share for younger firms. Moreover, most of the job creation by young firms occurs in the expanding service sector. We discuss different explanations for why Sweden appears not to have the same strong decline in entrepreneurial activity as the U.S. has had during the last two decades. We argue that one important explanation is the economic reforms that were implemented in Sweden in the 1990s that mitigated several hurdles to entrepreneurship.
  • Karlsson, Fredrik, et al. (författare)
  • Sensor Fused Indoor Positioning Using Dual Band WiFi Signal Measurements
  • 2015
  • Ingår i: 2015 European Control Conference (ECC). - IEEE - Institute of Electrical and Electronics Engineers Inc.. - 978-3-9524-2693-7 ; s. 1669-1672
  • Konferensbidrag (refereegranskat)abstract
    • In this paper, signal strengths from known WiFi access points are used together with a particle filter to perform indoor navigation. It is shown that more information is obtained by using signals of both 2.4 and 5.0 GHz, compared to using only one frequency. Thus, using both frequencies provides a more accurate positioning. The second contribution is an algorithm where WiFi measurements are combined with pedestrian dead reckoning (PDR), which is based on step counting using an accelerometer and hypotheses of the heading using a gyroscope. This was found to provide further accuracy compared to more conventional methods.
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